- Ifeffit - millenia.cars.aps.anl.gov

Normalization of LCF coefficients when fitting experimental spectra with theoretical spectra
by Patricia Poths 11 Mar '21

11 Mar '21

Hi, I am a theoretical chemistry PhD student working on fitting experimental spectra with computed spectra in order to get a better understanding of the composition. In the LCF process with athena, I have found that when I allow "sum coefficients to 1", I get an unphysical negative coefficient of the last standard- after reading through the mailing list I understood why, and so no longer use that. The sum of my coefficients during the fitting now is close to 1- generally within the range of 0.95-1.1 at the absolute extremes, but more often around ~0.98- ~1.05. In order to compare these coefficients, I renormalize them to 1, so they can represent the fractions of each component present. However, to test this I took the new normalized coefficients and summed up the standards with their respective weights to create this normalized "fit", and found that it is worse than the initial one. Is this something I should be concerned about when reporting the qualitative trends in how the composition changes? And if so, is there a better way to do the fits in a more normalized way? Many thanks, Patricia

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Re: [Ifeffit] Ifeffit Digest, Vol 217, Issue 6
by Clark Adam Hugh (PSI) 10 Mar '21

10 Mar '21

Dear Valerie Sorry! I don't know where I got the idea that it was Fe, I was probably working on Fe data at the time of writing. Having looked back I can see Mo. "I am using Larch XAS Viewer for the first time to analyze some Mo XANES data. It is fairly straightforward, however I am running into problems with energy calibration, which leads to problems with Linear Combination Fitting." For Mo I also have some standards, maybe these would be helpful for you. These are all calibrated with the first derivative of the Mo foil and so are consistent with each other. Although measured on a different monochromator, the likely would serve well to compare the edge position to make sure the calibration is done consistently for the standards you have from the canadian light source to give some idea of if things are reliable. Si(111): Mo MoO2 MoO3 Fe2Mo3O12 Mo2C NiMoO4 Adam __________________________________________ Paul Scherrer Institut Adam Hugh Clark WLGA/129 Forschungsstrasse 111 5232 Villigen PSI Schweiz Telefon: +41 56 310 41 51 E-Mail: adam.clark(a)psi.ch ________________________________ From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> on behalf of ifeffit-request(a)millenia.cars.aps.anl.gov <ifeffit-request(a)millenia.cars.aps.anl.gov> Sent: Tuesday, March 9, 2021 7:00:01 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 217, Issue 6 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. Re: Re. Larch Energy Calibration (Mangold, Stefan (IPS)) 2. Re: Larch Energy calibration (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Tue, 9 Mar 2021 11:20:38 +0000 From: "Mangold, Stefan (IPS)" <stefan.mangold(a)kit.edu> To: "Schoepfer, Valerie" <valerie.schoepfer(a)usask.ca> Cc: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Re. Larch Energy Calibration Message-ID: <45116D6C-9314-4822-8E1B-7FB929333D72(a)kit.edu> Content-Type: text/plain; charset="utf-8" Dear Valerie, The reason why I'm currently not using Larch for my data-evaluation chain is, that I didn?t found some features (like energy calibration; not as I use it; like Calibration of references, absorption and fluorescence spectra in one group) in Larch, which I need for my data evaluation process. They might be there, but I didn?t found them. for the XANES data evaluation your energy region might be a bit to short to fit a good background to the data. Anyway you have to fine-tune the parameters to reach a good background fit in the XANES region. While the automatic process in Athena produces quite good results for a lot of absorption edges, one has to be careful not add artefacts to the data in the XANES. Best regards Stefan > Am 08.03.2021 um 14:17 schrieb Schoepfer, Valerie <valerie.schoepfer(a)usask.ca>: > > Hi Chris and Adam, > > I'm actually looking at Mo, so the energy range is from about 19800 through 20200 eV on a Si(220) monochromator. (But thank you for your Fe offer!) > The standards seem to be all from the Canadian Light Source, but going as far back as 2013... > I'm not looking to make the LCF perfect at this point, but it does seem like the deeper I go, the less confident I am that I have the correct standards. > > I'm doing alright in Athena with respect to the process, its just that I can't get Larch to align properly. I'll probably just use Athena for data prep, Larch just seemed nice to learn. > But then in Athena I run into trouble with incorrect standards. One thing after another, you know? > > Thanks- > Valerie > > -----Original Message----- > From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov > Sent: Thursday, March 4, 2021 12:00 PM > To: ifeffit(a)millenia.cars.aps.anl.gov > Subject: Ifeffit Digest, Vol 217, Issue 3 > > CAUTION: External to USask. Verify sender and use caution with links and attachments. Forward suspicious emails to phishing(a)usask.ca > > > Send Ifeffit mailing list submissions to > ifeffit(a)millenia.cars.aps.anl.gov > > To subscribe or unsubscribe via the World Wide Web, visit > http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit > or, via email, send a message with subject or body 'help' to > ifeffit-request(a)millenia.cars.aps.anl.gov > > You can reach the person managing the list at > ifeffit-owner(a)millenia.cars.aps.anl.gov > > When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." > > > Today's Topics: > > 1. Re: Larch energy calibration (Matt Newville) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Wed, 3 Mar 2021 18:38:24 -0600 > From: Matt Newville <newville(a)cars.uchicago.edu> > To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> > Subject: Re: [Ifeffit] Larch energy calibration > Message-ID: > <CA+7ESbrGYtdjidL4X+rCUEi+DfmL3dUyG-R2R-FHffeqshSGTQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Valerie, > > On Tue, Mar 2, 2021 at 10:48 AM Schoepfer, Valerie < valerie.schoepfer(a)usask.ca> wrote: > >> Hi, >> >> >> >> I am using Larch XAS Viewer for the first time to analyze some Mo >> XANES data. It is fairly straightforward, however I am running into >> problems with energy calibration, which leads to problems with Linear >> Combination Fitting. >> >> >> >> Right now, which is likely wrong, I?m calibrating the energy of a >> standard to the theoretical edge, then auto-aligning the samples to the standard. >> But how do reference foils fit in here? Reference foils don?t seem to >> be tied to the sample like they are in Athena. Should I be manually aligning? >> >> >> >> Is there a general guidance or work flow? >> > > It's possible that I do not fully understand the question or that this answer will veer a bit off the topic of your question. > > For sure, energies need to be aligned properly for any multi-spectra comparison or linear method to work well. But it should be that you will have groups of spectra that all share a consistent energy calibration, say from the same beamline/beamtime. > > If you do have a reference channel for every measurement, you can compare those reference channels. Ideally, these will not vary for every > measurement - that would indicate a serious problem. So, I think you > should be able to group spectra together as uniformly calibrated (hopefully all data from a day or more of beamtime at a particular beamline) and then make sure that the different groups of spectra. Does that seem reasonable? > > I have to admit that at my beamline I don't often have the luxury or need to run a reference foil for every scan, so we calibrate consistently ahead > of time. I'm sure that leads to a bias in the software. I guess I forgot > that Athena had the ability to read and tie a second spectrum as a "reference" and use that to auto-apply calibration. > > Is it generally necessary to calibrate many spectra individually, or do people find that doing them in a few large groups is sufficient? > > --Matt >

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Re: [Ifeffit] Larch Energy calibration
by Schoepfer, Valerie 09 Mar '21

09 Mar '21

Hi Matt, The backstory is that I'm trying to find which standards will define my samples, so I am pulling standards from different beamlines and years to get a basic linear combination fit, to run new standards myself when I have more beamtime. I'm able to do it in Athena- where you more or less: 1. Assign E0 to the first peak in the first derivative of your standard reference foil. 2. Calibrate one standard reference foil to the theoretical edge energy. 3. Ensure E0 is right/adjust E0 for all samples and sample foils. 4. Align reference foils to the standard reference foil, because the foil will pull the sample with it. But in Larch, maybe I'm unsure about the groups function? I'm not convinced the reference foils 'follow' the sample spectra. If the reference and samples aren't tied together, how do you align samples when your energies are off because of different beamlines or years or people not as careful to calibrate the beamline energy? My first thought was using the first derivative peak of your sample, but if your edge energy shifts because of oxidation state changes, what do you use then? I'm still trying to form my question, so let me know if this still doesn't make much sense. Thanks! Valerie -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Thursday, March 4, 2021 12:00 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 217, Issue 3 CAUTION: External to USask. Verify sender and use caution with links and attachments. Forward suspicious emails to phishing(a)usask.ca Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. Re: Larch energy calibration (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Wed, 3 Mar 2021 18:38:24 -0600 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Larch energy calibration Message-ID: <CA+7ESbrGYtdjidL4X+rCUEi+DfmL3dUyG-R2R-FHffeqshSGTQ(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Valerie, On Tue, Mar 2, 2021 at 10:48 AM Schoepfer, Valerie < valerie.schoepfer(a)usask.ca> wrote: > Hi, > > > > I am using Larch XAS Viewer for the first time to analyze some Mo > XANES data. It is fairly straightforward, however I am running into > problems with energy calibration, which leads to problems with Linear > Combination Fitting. > > > > Right now, which is likely wrong, I?m calibrating the energy of a > standard to the theoretical edge, then auto-aligning the samples to the standard. > But how do reference foils fit in here? Reference foils don?t seem to > be tied to the sample like they are in Athena. Should I be manually aligning? > > > > Is there a general guidance or work flow? > It's possible that I do not fully understand the question or that this answer will veer a bit off the topic of your question. For sure, energies need to be aligned properly for any multi-spectra comparison or linear method to work well. But it should be that you will have groups of spectra that all share a consistent energy calibration, say from the same beamline/beamtime. If you do have a reference channel for every measurement, you can compare those reference channels. Ideally, these will not vary for every measurement - that would indicate a serious problem. So, I think you should be able to group spectra together as uniformly calibrated (hopefully all data from a day or more of beamtime at a particular beamline) and then make sure that the different groups of spectra. Does that seem reasonable? I have to admit that at my beamline I don't often have the luxury or need to run a reference foil for every scan, so we calibrate consistently ahead of time. I'm sure that leads to a bias in the software. I guess I forgot that Athena had the ability to read and tie a second spectrum as a "reference" and use that to auto-apply calibration. Is it generally necessary to calibrate many spectra individually, or do people find that doing them in a few large groups is sufficient? --Matt

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Re. Larch Energy Calibration
by Schoepfer, Valerie 09 Mar '21

09 Mar '21

Hi Chris and Adam, I'm actually looking at Mo, so the energy range is from about 19800 through 20200 eV on a Si(220) monochromator. (But thank you for your Fe offer!) The standards seem to be all from the Canadian Light Source, but going as far back as 2013... I'm not looking to make the LCF perfect at this point, but it does seem like the deeper I go, the less confident I am that I have the correct standards. I'm doing alright in Athena with respect to the process, its just that I can't get Larch to align properly. I'll probably just use Athena for data prep, Larch just seemed nice to learn. But then in Athena I run into trouble with incorrect standards. One thing after another, you know? Thanks- Valerie -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Thursday, March 4, 2021 12:00 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 217, Issue 3 CAUTION: External to USask. Verify sender and use caution with links and attachments. Forward suspicious emails to phishing(a)usask.ca Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. Re: Larch energy calibration (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Wed, 3 Mar 2021 18:38:24 -0600 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Larch energy calibration Message-ID: <CA+7ESbrGYtdjidL4X+rCUEi+DfmL3dUyG-R2R-FHffeqshSGTQ(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Valerie, On Tue, Mar 2, 2021 at 10:48 AM Schoepfer, Valerie < valerie.schoepfer(a)usask.ca> wrote: > Hi, > > > > I am using Larch XAS Viewer for the first time to analyze some Mo > XANES data. It is fairly straightforward, however I am running into > problems with energy calibration, which leads to problems with Linear > Combination Fitting. > > > > Right now, which is likely wrong, I?m calibrating the energy of a > standard to the theoretical edge, then auto-aligning the samples to the standard. > But how do reference foils fit in here? Reference foils don?t seem to > be tied to the sample like they are in Athena. Should I be manually aligning? > > > > Is there a general guidance or work flow? > It's possible that I do not fully understand the question or that this answer will veer a bit off the topic of your question. For sure, energies need to be aligned properly for any multi-spectra comparison or linear method to work well. But it should be that you will have groups of spectra that all share a consistent energy calibration, say from the same beamline/beamtime. If you do have a reference channel for every measurement, you can compare those reference channels. Ideally, these will not vary for every measurement - that would indicate a serious problem. So, I think you should be able to group spectra together as uniformly calibrated (hopefully all data from a day or more of beamtime at a particular beamline) and then make sure that the different groups of spectra. Does that seem reasonable? I have to admit that at my beamline I don't often have the luxury or need to run a reference foil for every scan, so we calibrate consistently ahead of time. I'm sure that leads to a bias in the software. I guess I forgot that Athena had the ability to read and tie a second spectrum as a "reference" and use that to auto-apply calibration. Is it generally necessary to calibrate many spectra individually, or do people find that doing them in a few large groups is sufficient? --Matt

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Re: [Ifeffit] Ifeffit Digest, Vol 217, Issue 4
by Clark Adam Hugh (PSI) 08 Mar '21

08 Mar '21

Dear Valerie Which Fe standards are you looking to compare? I have a large collection of Fe references collected from the SuperXAS beamline all relatively recently and are all calibrated using Fe reference foil measured simultaneously. Using a Si(111) monochromator: Fe2O3 Fe3C Fe5C2 Fe3O4 FeO Ferrihydrite Goethite Lepidrocrite FeCl3.xH2O FeCl2 FeSO4 FeAmmoniumSulfate Fe_Nitrate Using Si(311) monochromator: FeO Fe2O3 Geothite Lepidrocrite Ferrihydrite FeIII_Hexacyanoferrate Fephthalocyanine Fetetraohenylporphyrine FePhenanthroline Fephthalocyanine chloride FeII_Hexacyanoferrate FeBisglycinate FeAmmoniumSulfate Fe2EDTA Fe3EDTA The monochromator crystal choice affects the shape of the XANES due to the relative energy resolution of the crystal. Regards Adam __________________________________________ Paul Scherrer Institut Adam Hugh Clark WLGA/129 Forschungsstrasse 111 5232 Villigen PSI Schweiz Telefon: +41 56 310 41 51 E-Mail: adam.clark(a)psi.ch -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Freitag, 5. März 2021 17:58 To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 217, Issue 4 Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. Re: Larch Energy calibration (Schoepfer, Valerie) 2. Re: Larch Energy calibration (Christopher Patridge) ---------------------------------------------------------------------- Message: 1 Date: Fri, 5 Mar 2021 16:06:22 +0000 From: "Schoepfer, Valerie" <valerie.schoepfer(a)usask.ca> To: "ifeffit(a)millenia.cars.aps.anl.gov" <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Larch Energy calibration Message-ID: <YTBPR01MB27659005C1015912348BA93894969(a)YTBPR01MB2765.CANPRD01.PROD.OUTLOOK.COM> Content-Type: text/plain; charset="us-ascii" Hi Matt, The backstory is that I'm trying to find which standards will define my samples, so I am pulling standards from different beamlines and years to get a basic linear combination fit, to run new standards myself when I have more beamtime. I'm able to do it in Athena- where you more or less: 1. Assign E0 to the first peak in the first derivative of your standard reference foil. 2. Calibrate one standard reference foil to the theoretical edge energy. 3. Ensure E0 is right/adjust E0 for all samples and sample foils. 4. Align reference foils to the standard reference foil, because the foil will pull the sample with it. But in Larch, maybe I'm unsure about the groups function? I'm not convinced the reference foils 'follow' the sample spectra. If the reference and samples aren't tied together, how do you align samples when your energies are off because of different beamlines or years or people not as careful to calibrate the beamline energy? My first thought was using the first derivative peak of your sample, but if your edge energy shifts because of oxidation state changes, what do you use then? I'm still trying to form my question, so let me know if this still doesn't make much sense. Thanks! Valerie -----Original Message----- From: Ifeffit <ifeffit-bounces(a)millenia.cars.aps.anl.gov> On Behalf Of ifeffit-request(a)millenia.cars.aps.anl.gov Sent: Thursday, March 4, 2021 12:00 PM To: ifeffit(a)millenia.cars.aps.anl.gov Subject: Ifeffit Digest, Vol 217, Issue 3 CAUTION: External to USask. Verify sender and use caution with links and attachments. Forward suspicious emails to phishing(a)usask.ca Send Ifeffit mailing list submissions to ifeffit(a)millenia.cars.aps.anl.gov To subscribe or unsubscribe via the World Wide Web, visit http://millenia.cars.aps.anl.gov/mailman/listinfo/ifeffit or, via email, send a message with subject or body 'help' to ifeffit-request(a)millenia.cars.aps.anl.gov You can reach the person managing the list at ifeffit-owner(a)millenia.cars.aps.anl.gov When replying, please edit your Subject line so it is more specific than "Re: Contents of Ifeffit digest..." Today's Topics: 1. Re: Larch energy calibration (Matt Newville) ---------------------------------------------------------------------- Message: 1 Date: Wed, 3 Mar 2021 18:38:24 -0600 From: Matt Newville <newville(a)cars.uchicago.edu> To: XAFS Analysis using Ifeffit <ifeffit(a)millenia.cars.aps.anl.gov> Subject: Re: [Ifeffit] Larch energy calibration Message-ID: <CA+7ESbrGYtdjidL4X+rCUEi+DfmL3dUyG-R2R-FHffeqshSGTQ(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hi Valerie, On Tue, Mar 2, 2021 at 10:48 AM Schoepfer, Valerie < valerie.schoepfer(a)usask.ca> wrote: > Hi, > > > > I am using Larch XAS Viewer for the first time to analyze some Mo > XANES data. It is fairly straightforward, however I am running into > problems with energy calibration, which leads to problems with Linear > Combination Fitting. > > > > Right now, which is likely wrong, I?m calibrating the energy of a > standard to the theoretical edge, then auto-aligning the samples to the standard. > But how do reference foils fit in here? Reference foils don?t seem to > be tied to the sample like they are in Athena. Should I be manually aligning? > > > > Is there a general guidance or work flow? > It's possible that I do not fully understand the question or that this answer will veer a bit off the topic of your question. For sure, energies need to be aligned properly for any multi-spectra comparison or linear method to work well. But it should be that you will have groups of spectra that all share a consistent energy calibration, say from the same beamline/beamtime. If you do have a reference channel for every measurement, you can compare those reference channels. Ideally, these will not vary for every measurement - that would indicate a serious problem. So, I think you should be able to group spectra together as uniformly calibrated (hopefully all data from a day or more of beamtime at a particular beamline) and then make sure that the different groups of spectra. Does that seem reasonable? I have to admit that at my beamline I don't often have the luxury or need to run a reference foil for every scan, so we calibrate consistently ahead of time. I'm sure that leads to a bias in the software. I guess I forgot that Athena had the ability to read and tie a second spectrum as a "reference" and use that to auto-apply calibration. Is it generally necessary to calibrate many spectra individually, or do people find that doing them in a few large groups is sufficient? --Matt

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Larch energy calibration
by Schoepfer, Valerie 03 Mar '21

03 Mar '21

Hi, I am using Larch XAS Viewer for the first time to analyze some Mo XANES data. It is fairly straightforward, however I am running into problems with energy calibration, which leads to problems with Linear Combination Fitting. Right now, which is likely wrong, I'm calibrating the energy of a standard to the theoretical edge, then auto-aligning the samples to the standard. But how do reference foils fit in here? Reference foils don't seem to be tied to the sample like they are in Athena. Should I be manually aligning? Is there a general guidance or work flow? Thank you- Valerie Valerie Schoepfer, PhD Postdoctoral Fellow Department of Geological Sciences [cid:image001.jpg@01D5CBC1.8203C730]

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Athena plugin for synchrotrons in Japan
by Yohei Uemura 01 Mar '21

01 Mar '21

Dear Bruce, This is Yohei Uemura. We are using the Athena plugin to read the data format used in synchrotrons in Japan. It is very helpful to read XAFS data directly into Athena. We appreciate the plugin. Recently, we realised that the plugin does not work properly for some data sets. When the data is like below (I0 and I are integers), the plugin works fine. Step scan (or QXAFS) using a counter device [image: image.png] However, if the data is like below (I0 and I are decimal fractions), the outputs of I0 and I are 4digit such as 0.345. QXAFS: I0 and I are decimal fractions [image: image.png] I found the problem was at l. 63. my $pattern = " %9.3f %9.3f %10.6f" . " %12.3f" x $ndet . $/; The output data is terminated by 3 digits after a decimal point. If the plugin is modified as the attached file, both the files were read correctly. The modification is: my $pattern = " %9.3f %9.3f %10.6f" . " %12.3f" x $ndet . $/; *$pattern = " %9.3f %9.3f %10.6f" . " %12.6f" x $ndet . $/ if $list[2+$ndet] =~ m/\d*\.\d+/;* I added the bolded line in order not to truncate the I0 and I by 3 digits. Could you modify the plugin which is provided with the demeter package? Best regards, Yohei -- ================================================ Yohei Uemura (Ph.D) Affiliation : Paul Scherrer Institut (PSI), Laboratory for Environmental Chemistry (LUC) Address : OFLB 106 (PSI Ost), PSI, Forschungsstrasse 111, 5232 Villigen, Switzerland Phone: +41 (0)5-6310-4571 上村洋平所属 : Paul Scherrer Institut (PSI), Laboratory for Environmental Chemistry (LUC) 住所 : OFLB 106 (PSI Ost), PSI, Forschungsstrasse 111, 5232 Villigen, Switzerland 電話 : +41 (0)5-6310-4571 ================================================

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postdoc opportunity at LANL
by Hickam, Sarah Margaret 03 Feb '21

03 Feb '21

Dear all, Los Alamos National Laboratory currently has a postdoc position open for xafs studies of actinide materials. The posting can be found at the following link: https://lanl.jobs/los-alamos-nm/nuclear-forensicsactinide-research-postdoc/… Please feel free to forward this to anyone who might be interested or contact me with any questions. Best regards, Sarah Sarah Hickam Postdoctoral Research Associate Los Alamos National Laboratory MST-16 (505) 695-3515

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Nanocrystalline NiO
by Christian Wittee Lopes 18 Jan '21

18 Jan '21

Dear all, Firstly I would like to wish you a much better year than in 2020. Does anyone have some spectra of nanocrystalline NiO (not bulk standards)? I have a spectrum of a mixed compound and would like to get more insights into what I really have in this sample. Thank you in advance!!! Kind regards, -- *Christian Wittee Lopes* *Visiting Researcher* ANP/FINEP - PRH50 Institute of Chemistry, Universidade Federal do Rio Grande do Sul (UFRGS) Phone: +55 54 992430264

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Larch: AttributeError
by Rachita Rana 13 Jan '21

13 Jan '21

Hi Everyone, I am using Larch for reading and fitting EXAFS data and I get the autobk and Fourier transforms working. But when I try to generate the fefffpaths and fit the data I get an error from the feffit function. I am using the developer version of Larch on MC OS Catalina. Below is the error and the sample script- runfile('/Users/rachita/Box/Larch/Feff_Try2/001.py', wdir='/Users/rachita/Box/Larch/Feff_Try2') Traceback (most recent call last): File "/Users/rachita/Box/Larch/Feff_Try2/001.py", line 27, in <module> fit = feffit(params, dset) File "/Users/rachita/opt/anaconda3/lib/python3.8/site-packages/xraylarch-0.9.50-py3.8.egg/larch/xafs/feffit.py", line 534, in feffit ds.prepare_fit(params=params) File "/Users/rachita/opt/anaconda3/lib/python3.8/site-packages/xraylarch-0.9.50-py3.8.egg/larch/xafs/feffit.py", line 265, in prepare_fit ikmax = int(1.01 + max(self.data.k)/trans.kstep) AttributeError: 'AthenaGroup' object has no attribute ‘k’ #tried this with xdi format data and got the same error Below is the script - #!/usr/bin/env python3 # -*- coding: utf-8 -*- from larch.fitting import param_group, Parameter from larch.io <http://larch.io/> import read_xdi from larch.xafs import feffpath, feffit_dataset, feffit_transform, feffit, feffit_report data = read_xdi('cu_metal_rt.xdi’) #I tried importing Athena project file too path1 = feffpath('feff0001.dat', s02='amplitude', e0='del_e0', sigma2='sigma2', deltar='del_r') trans = feffit_transform(kmin=3, kmax=16, kw=(2,1,3), dk=1, window='hanning', rmin=1.7, rmax=3.1) params = param_group(amplitude= Parameter(1, vary=True), del_e0 = Parameter(1e-7, vary=True), del_r = Parameter(1e-7, vary=True), sigma2 = Parameter(0.003, vary=True)) dset = feffit_dataset(data=data, pathlist=[path1], transform=trans) fit = feffit(params, dset) print(feffit_report(fit)) By printing path groups and transform fit, I confirmed that the data is read correctly. Please let me know if there are ways to fix this or if there is an error in my script. Thank You! Rachita

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